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Mediator of RNA polymerase II transcription subunit 18 (Mediator complex subunit 18) (Suppressor of RNA polymerase B 5)

 MED18_YEAST             Reviewed;         307 AA.
P32585; D6VUN6; Q6B1R3;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
01-OCT-1993, sequence version 1.
25-OCT-2017, entry version 149.
RecName: Full=Mediator of RNA polymerase II transcription subunit 18;
AltName: Full=Mediator complex subunit 18;
AltName: Full=Suppressor of RNA polymerase B 5;
Name=SRB5; Synonyms=MED18; OrderedLocusNames=YGR104C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND MUTAGENESIS OF THR-22.
STRAIN=Z28;
PubMed=8324825; DOI=10.1016/0092-8674(93)90362-T;
Thompson C.M., Koleske A.J., Chao D.M., Young R.A.;
"A multisubunit complex associated with the RNA polymerase II CTD and
TATA-binding protein in yeast.";
Cell 73:1361-1375(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169869;
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M.,
Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J.,
Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E.,
Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E.,
Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B.,
Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L.,
Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M.,
Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M.,
Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B.,
Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W.,
Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A.,
Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S.,
Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L.,
Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S.,
Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J.,
Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M.,
Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B.,
Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J.,
Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M.,
van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M.,
Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H.,
Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M.,
Zollner A., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[5]
COMPONENT OF MEDIATOR COMPLEX.
PubMed=8187178; DOI=10.1016/0092-8674(94)90221-6;
Kim Y.-J., Bjoerklund S., Li Y., Sayre M.H., Kornberg R.D.;
"A multiprotein mediator of transcriptional activation and its
interaction with the C-terminal repeat domain of RNA polymerase II.";
Cell 77:599-608(1994).
[6]
FUNCTION.
PubMed=9845373; DOI=10.1016/S0092-8674(00)81641-4;
Holstege F.C.P., Jennings E.G., Wyrick J.J., Lee T.I.,
Hengartner C.J., Green M.R., Golub T.R., Lander E.S., Young R.A.;
"Dissecting the regulatory circuitry of a eukaryotic genome.";
Cell 95:717-728(1998).
[7]
INTERACTION WITH SRB2.
PubMed=9660972; DOI=10.1016/S1097-2765(00)80088-X;
Koh S.S., Ansari A.Z., Ptashne M., Young R.A.;
"An activator target in the RNA polymerase II holoenzyme.";
Mol. Cell 1:895-904(1998).
[8]
INTERACTION WITH MED8, FUNCTION OF THE MEDIATOR COMPLEX, AND
INTERACTION OF THE MEDIATOR COMPLEX WITH RNA POLYMERASE II.
PubMed=11555651; DOI=10.1074/jbc.M105961200;
Kang J.S., Kim S.H., Hwang M.S., Han S.J., Lee Y.C., Kim Y.-J.;
"The structural and functional organization of the yeast mediator
complex.";
J. Biol. Chem. 276:42003-42010(2001).
[9]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[10]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[11]
NOMENCLATURE.
PubMed=15175151; DOI=10.1016/j.molcel.2004.05.011;
Bourbon H.-M., Aguilera A., Ansari A.Z., Asturias F.J., Berk A.J.,
Bjoerklund S., Blackwell T.K., Borggrefe T., Carey M., Carlson M.,
Conaway J.W., Conaway R.C., Emmons S.W., Fondell J.D., Freedman L.P.,
Fukasawa T., Gustafsson C.M., Han M., He X., Herman P.K.,
Hinnebusch A.G., Holmberg S., Holstege F.C.P., Jaehning J.A.,
Kim Y.-J., Kuras L., Leutz A., Lis J.T., Meisterernest M.,
Naeaer A.M., Nasmyth K., Parvin J.D., Ptashne M., Reinberg D.,
Ronne H., Sadowski I., Sakurai H., Sipiczki M., Sternberg P.W.,
Stillman D.J., Strich R., Struhl K., Svejstrup J.Q., Tuck S.,
Winston F., Roeder R.G., Kornberg R.D.;
"A unified nomenclature for protein subunits of mediator complexes
linking transcriptional regulators to RNA polymerase II.";
Mol. Cell 14:553-557(2004).
[12]
TOPOLOGY OF THE MEDIATOR COMPLEX.
PubMed=15477388; DOI=10.1093/nar/gkh878;
Guglielmi B., van Berkum N.L., Klapholz B., Bijma T., Boube M.,
Boschiero C., Bourbon H.-M., Holstege F.C.P., Werner M.;
"A high resolution protein interaction map of the yeast Mediator
complex.";
Nucleic Acids Res. 32:5379-5391(2004).
[13]
CHARACTERIZATION OF THE MEDIATOR COMPLEX.
PubMed=16002404; DOI=10.1074/jbc.C500150200;
Takagi Y., Chadick J.Z., Davis J.A., Asturias F.J.;
"Preponderance of free mediator in the yeast Saccharomyces
cerevisiae.";
J. Biol. Chem. 280:31200-31207(2005).
[14]
FUNCTION OF THE MEDIATOR COMPLEX.
PubMed=16076843; DOI=10.1074/jbc.M506067200;
Nair D., Kim Y., Myers L.C.;
"Mediator and TFIIH govern carboxyl-terminal domain-dependent
transcription in yeast extracts.";
J. Biol. Chem. 280:33739-33748(2005).
[15]
FUNCTION.
PubMed=16109375; DOI=10.1016/j.molcel.2005.06.033;
van de Peppel J., Kettelarij N., van Bakel H., Kockelkorn T.T.J.P.,
van Leenen D., Holstege F.C.P.;
"Mediator expression profiling epistasis reveals a signal transduction
pathway with antagonistic submodules and highly specific downstream
targets.";
Mol. Cell 19:511-522(2005).
[16]
FUNCTION OF THE MEDIATOR COMPLEX.
PubMed=16263706; DOI=10.1074/jbc.M508253200;
Takagi Y., Kornberg R.D.;
"Mediator as a general transcription factor.";
J. Biol. Chem. 281:80-89(2006).
[17]
INTERACTION WITH MED1; MED8; CSE2 AND RGR1, CHARACTERIZATION OF THE
MEDIATOR COMPLEX, AND INTERACTION OF THE MEDIATOR COMPLEX WITH RNA
POLYMERASE II.
PubMed=17192271; DOI=10.1074/jbc.M609484200;
Baidoobonso S.M., Guidi B.W., Myers L.C.;
"Med19(Rox3) regulates intermodule interactions in the Saccharomyces
cerevisiae mediator complex.";
J. Biol. Chem. 282:5551-5559(2007).
[18]
ELECTRON MICROSCOPY OF MEDIATOR COMPLEX IN COMPLEX WITH RNA POLYMERASE
II.
PubMed=12191485; DOI=10.1016/S1097-2765(02)00598-1;
Davis J.A., Takagi Y., Kornberg R.D., Asturias F.J.;
"Structure of the yeast RNA polymerase II holoenzyme: mediator
conformation and polymerase interaction.";
Mol. Cell 10:409-415(2002).
[19]
ELECTRON MICROSCOPY OF THE MEDIATOR COMPLEX HEAD MODULE, FUNCTION OF
THE MEDIATOR COMPLEX HEAD MODULE, INTERACTION OF THE MEDIATOR COMPLEX
HEAD MODULE WITH RNA POLYMERASE II AND TFIIF, AND INTERACTION WITH
SRB2 AND SRB4.
PubMed=16885025; DOI=10.1016/j.molcel.2006.06.007;
Takagi Y., Calero G., Komori H., Brown J.A., Ehrensberger A.H.,
Hudmon A., Asturias F.J., Kornberg R.D.;
"Head module control of mediator interactions.";
Mol. Cell 23:355-364(2006).
[20]
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 2-307 IN COMPLEX WITH MED8
AND SRB2.
PubMed=16964259; DOI=10.1038/nsmb1143;
Lariviere L., Geiger S., Hoeppner S., Roether S., Straesser K.,
Cramer P.;
"Structure and TBP binding of the Mediator head subcomplex Med8-Med18-
Med20.";
Nat. Struct. Mol. Biol. 13:895-901(2006).
-!- FUNCTION: Component of the Mediator complex, a coactivator
involved in the regulated transcription of nearly all RNA
polymerase II-dependent genes. Mediator functions as a bridge to
convey information from gene-specific regulatory proteins to the
basal RNA polymerase II transcription machinery. The Mediator
complex, having a compact conformation in its free form, is
recruited to promoters by direct interactions with regulatory
proteins and serves for the assembly of a functional preinitiation
complex with RNA polymerase II and the general transcription
factors. The Mediator complex unfolds to an extended conformation
and partially surrounds RNA polymerase II, specifically
interacting with the unphosphorylated form of the C-terminal
domain (CTD) of RNA polymerase II. The Mediator complex
dissociates from the RNA polymerase II holoenzyme and stays at the
promoter when transcriptional elongation begins.
{ECO:0000269|PubMed:11555651, ECO:0000269|PubMed:16076843,
ECO:0000269|PubMed:16109375, ECO:0000269|PubMed:16263706,
ECO:0000269|PubMed:16885025, ECO:0000269|PubMed:9845373}.
-!- SUBUNIT: Component of the Mediator complex, which is composed of
at least 21 subunits that form three structurally distinct
submodules. The Mediator head module contains MED6, MED8, MED11,
SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22, the
middle module contains MED1, MED4, NUT1/MED5, MED7, CSE2/MED9,
NUT2/MED10, SRB7/MED21 and SOH1/MED31, and the tail module
contains MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16.
The head and the middle modules interact directly with RNA
polymerase II, whereas the elongated tail module interacts with
gene-specific regulatory proteins. SRB5/MED18 interacts directly
with MED8 and SRB2/MED20. {ECO:0000269|PubMed:11555651,
ECO:0000269|PubMed:16885025, ECO:0000269|PubMed:16964259,
ECO:0000269|PubMed:17192271, ECO:0000269|PubMed:9660972}.
-!- INTERACTION:
P38304:MED8; NbExp=8; IntAct=EBI-18032, EBI-20932;
P34162:SRB2; NbExp=6; IntAct=EBI-18032, EBI-18018;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 1011 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the Mediator complex subunit 18 family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; L12028; AAB08012.1; -; Genomic_DNA.
EMBL; Z72889; CAA97108.1; -; Genomic_DNA.
EMBL; AY693017; AAT93036.1; -; Genomic_DNA.
EMBL; BK006941; DAA08197.1; -; Genomic_DNA.
PIR; B40711; B40711.
RefSeq; NP_011618.3; NM_001181233.3.
PDB; 2HZM; X-ray; 2.40 A; B/D/F/H=2-307.
PDB; 2HZS; X-ray; 2.70 A; B/D/F/H=2-307.
PDB; 3J1O; EM; 16.00 A; L=1-307.
PDB; 3RJ1; X-ray; 4.30 A; E/L/S=1-307.
PDB; 4GWP; X-ray; 4.20 A; E=1-307.
PDB; 4GWQ; X-ray; 4.50 A; E=1-307.
PDB; 4V1O; EM; 9.70 A; X=1-307.
PDB; 5SVA; EM; 15.30 A; Q=1-307.
PDBsum; 2HZM; -.
PDBsum; 2HZS; -.
PDBsum; 3J1O; -.
PDBsum; 3RJ1; -.
PDBsum; 4GWP; -.
PDBsum; 4GWQ; -.
PDBsum; 4V1O; -.
PDBsum; 5SVA; -.
ProteinModelPortal; P32585; -.
SMR; P32585; -.
BioGrid; 33347; 92.
DIP; DIP-1658N; -.
IntAct; P32585; 32.
MINT; MINT-383791; -.
STRING; 4932.YGR104C; -.
MaxQB; P32585; -.
PRIDE; P32585; -.
EnsemblFungi; YGR104C; YGR104C; YGR104C.
GeneID; 852996; -.
KEGG; sce:YGR104C; -.
EuPathDB; FungiDB:YGR104C; -.
SGD; S000003336; SRB5.
HOGENOM; HOG000113528; -.
InParanoid; P32585; -.
KO; K15136; -.
OMA; PGKVNQI; -.
OrthoDB; EOG092C41CG; -.
BioCyc; YEAST:G3O-30814-MONOMER; -.
EvolutionaryTrace; P32585; -.
PRO; PR:P32585; -.
Proteomes; UP000002311; Chromosome VII.
GO; GO:0070847; C:core mediator complex; IDA:SGD.
GO; GO:0016592; C:mediator complex; IBA:GO_Central.
GO; GO:0000979; F:RNA polymerase II core promoter sequence-specific DNA binding; IDA:SGD.
GO; GO:0001104; F:RNA polymerase II transcription cofactor activity; IBA:GO_Central.
GO; GO:0001129; F:RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly; IDA:SGD.
GO; GO:0000991; F:transcription factor activity, core RNA polymerase II binding; IDA:SGD.
GO; GO:0001135; F:transcription factor activity, RNA polymerase II transcription factor recruiting; IMP:SGD.
GO; GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:SGD.
GO; GO:0051123; P:RNA polymerase II transcriptional preinitiation complex assembly; IDA:SGD.
GO; GO:0006369; P:termination of RNA polymerase II transcription; IMP:SGD.
GO; GO:0001113; P:transcriptional open complex formation at RNA polymerase II promoter; IMP:SGD.
InterPro; IPR019095; Mediator_Med18_met/fun.
Pfam; PF09637; Med18; 1.
1: Evidence at protein level;
3D-structure; Activator; Complete proteome; Nucleus;
Reference proteome; Transcription; Transcription regulation.
CHAIN 1 307 Mediator of RNA polymerase II
transcription subunit 18.
/FTId=PRO_0000096368.
MUTAGEN 22 22 T->I: In SRB5-1; suppresses the
phenotypic defects of an RNA polymerase
II CTD truncation.
{ECO:0000269|PubMed:8324825}.
CONFLICT 225 225 K -> R (in Ref. 4; AAT93036).
{ECO:0000305}.
STRAND 3 12 {ECO:0000244|PDB:2HZM}.
HELIX 13 15 {ECO:0000244|PDB:2HZM}.
HELIX 16 27 {ECO:0000244|PDB:2HZM}.
STRAND 32 43 {ECO:0000244|PDB:2HZM}.
HELIX 45 47 {ECO:0000244|PDB:2HZM}.
STRAND 64 68 {ECO:0000244|PDB:2HZM}.
HELIX 72 74 {ECO:0000244|PDB:2HZM}.
HELIX 75 78 {ECO:0000244|PDB:2HZS}.
TURN 79 81 {ECO:0000244|PDB:2HZS}.
HELIX 87 92 {ECO:0000244|PDB:2HZM}.
STRAND 95 97 {ECO:0000244|PDB:2HZM}.
STRAND 164 170 {ECO:0000244|PDB:2HZM}.
HELIX 173 175 {ECO:0000244|PDB:2HZM}.
STRAND 180 195 {ECO:0000244|PDB:2HZM}.
HELIX 200 206 {ECO:0000244|PDB:2HZM}.
STRAND 209 223 {ECO:0000244|PDB:2HZM}.
HELIX 225 227 {ECO:0000244|PDB:2HZM}.
STRAND 229 239 {ECO:0000244|PDB:2HZM}.
STRAND 242 245 {ECO:0000244|PDB:2HZM}.
TURN 246 249 {ECO:0000244|PDB:2HZM}.
STRAND 250 259 {ECO:0000244|PDB:2HZM}.
HELIX 265 281 {ECO:0000244|PDB:2HZM}.
TURN 282 285 {ECO:0000244|PDB:2HZM}.
HELIX 293 297 {ECO:0000244|PDB:2HZM}.
HELIX 299 301 {ECO:0000244|PDB:2HZM}.
SEQUENCE 307 AA; 34289 MW; B1148FC187C2802A CRC64;
MVQQLSLFGS IGDDGYDLLI STLTTISGNP PLLYNSLCTV WKPNPSYDVE NVNSRNQLVE
PNRIKLSKEV PFSYLIDETM MDKPLNFRIL KSFTNDKIPL NYAMTRNILH NTVPQVTNFN
STNEDQNNSK HTEDTVNESR NSDDIIDVDM DASPAPSNES CSPWSLQISD IPAAGNNRSV
SMQTIAETII LSSAGKNSSV SSLMNGLGYV FEFQYLTIGV KFFMKHGLIL ELQKIWQIEE
AGNSQITSGG FLLKAYINVS RGTDIDRINY TETALMNLKK ELQGYIELSV PDRQSMDSRV
AHGNILI


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